Chuck Bartowski: Rogue Agent
by Spawn Hades
Summary: What if Chuck and Sarah rescued Orion and destroyed Fulcrum the same night they ran away together? What if when Casey reached Barstow, Chuck and Sarah where already dead. What if Chuck and Sarah went rogue to protect their loved ones? Well, read more and find out.
1. Chapter 1: Prologue

_**Disclaimer:**_ _ **I don't own "Chuck"**_

 _ **Chapter 1: Prologue**_

* * *

Chuck is extremely terrified as he and Sarah arrive at the motel, he knows that there is no going back. He knows that he will most likely never see Ellie again. He knows that if they fail, his father and most likely they, will die. So why is he doing this?

Because he is following his heart and his heart is telling him that if he wants to save his father and maybe possibly ever have a real relationship with Sarah, he CANNOT go to a bunker.

So here they are, at a motel on the side of the freeway, looking for a secret terrorist base. And it is not going well at all.

"Sarah there isn't anything here. What about that drive in theatre? If they are wanting to upload the Intersect to all of their agents at the same time, what better way than a huge screen at an abandoned theatre? It's perfect." Chuck suggests, now pulling at straws.

"Yes, Chuck you're a genius. But we need to be subtle, I say we book a room and wait until after midnight before sneaking out the back window because I've already noticed that we have a tail." She plans.

"Okay, let's do it." So they did exactly that. As they waited, they began to plan out what they would do if they somehow made it out of there alive and with Chuck's dad.

"I have an idea. I don't like it but I don't see any other way. Just don't hate me okay?" He bows his head in shame of what he is about to suggest.

"Chuck I could never hate you, so go ahead." She places her hand on his forearm to comfort.

"I say that we fake our deaths. We get my dad to order a predator drone strike, and we make it look like we were in the blast radius. It's the only way I can see us all getting out of this alive." He gives her a sad smile.

"Okay Chuck, we will go with your plan, I understand what you are giving up for this, but you know what this means don't you?" She asks. He simply nods.

"Chuck, if we do this there is no going back. Everyone we know are going to think we are dead and we can never tell them otherwise. You are never going to have that normal life that you always wanted." She frowns at that, remembering their talk at the fountain after the Van Hayes mission.

"I lied you know." Chuck says, breaking up the uncomfortable silence.

"What?" She asks, confused.

"Back when Bryce was in Burbank for the Von Hayes mission. I realise that I let him manipulate me into breaking up with you so that he could swoop in for the kill." He chuckles at that.

"What do you mean manipulate Chuck?" She asks, beginning to feel angry at Bryce for using Chuck.

"He told me that I had to break up with me so that you wouldn't get hurt because of your feelings towards me. I'm only now realising how stupid that sounds, I mean you guys surely had feelings for each other considering you were together when you were Grahams' best team." He gives her a big hearty laugh.

"Wow, Chuck. I don't know what to say to that." She was genuinely conflicted, one part of her brain was telling her to insult Chuck and tell him how much of an idiot he was for letting Bryce manipulate him. But her heart was telling her to kiss him for being such a nice guy always wanting to protect her, regardless how stupid he was in the way he did it.

For the first time in over a year, her heart won the fight and she kissed him gently. She didn't know how long they stayed like that, sitting on the couch, exchanging small kisses, but when they finally, reluctantly, pulled way… it was time for them to go.

* * *

"Okay… Wow, ummmm. We should probably go now…"She stuttered.

"Yeah… Uh can I have a request for if we survive this?" Chuck asks with a slight blush.

"Sure…" She waits for him to ask.

"Can we continue this?" He asks quietly.

"Chuck can I tell you something?" Sarah asks.

"Yeah?" He waits for her to finish.

"If we make it out of this alive, we will go much farther than what just happened." She smiles at him before standing up and heading to the bedside table and picking up two Smith & Wesson pistols and two Tranq Guns.

She walks back over to him and hand him the tranq guns. "Here, I saw how well you did back at RI from surveillance and I must say, you definitely have potential." She gives him a cheeky grin. "But you will definitely need some training. Especially if we are going to be on the run from the CIA, NSA and any other intelligence agency that learns about you." She changed to a serious demeanor for that last sentence.

"Okay, I guess it could be fun." Chuck wearily replies.

"Well, let's go save your dad Chuck." She smiles a genuine smile at him.

* * *

When they reached the theatre, they noticed an agent walk up to a kid's park and open a secret hatch in the ground. "Looks like we have found our bad guy base."

"Yes, it certainly does. Are you ready for this Chuck? Last chance o back out." She looks at him wearily.

"Let's do this." He says with determination.

When they open the hatch they both quickly and quietly make their way down the ladder. They begin to make their way through the hall, stopping only for Chuck to tranq guards as they rounded corners. When they eventually made it to the only room with a light coming from it, Chuck heard a voice through the doors.

"Charles, you can do this I believe in you."

Chuck nudged the door open ad saw that the only person in the room was Chuck's dad.

"Dad!" Chuck whispers excitedly.

"Hello Charles. I didn't expect you until tomorrow morning."

"Well, you can't always believe what a computer says, I should know, I am living proof that you should be wary about trusting a computer. Now let's get these chains off of you and get out of here. The quicker we can get on the road, the more of a head start against the CIA we will have." Chuck explains.

"I thought that you where rouge but one thing, why are you helping us Sarah?" Stephen asks.

"I… I… believe that Chuck doesn't deserve to be stuck in a bunker for the rest of his life. And he is… different from any other man I have ever met, he is… special." She rambles.

"That he is." The elder Bartowski gave Sarah a hug. Chuck had to turn away as he had a huge shit-eating grin plastered on his face.

"Guys, its show time. Dad grab the 2.0 please." Chuck orders with a soft tone, still not used to being a spy.

"Okay." The other two said at the same time, releasing their hug.

As the three made their way out the same way they came in, Chuck shot all of the already tranquilized fulcrum agents. The others look at him quizzically. "What? It can't hurt to be thorough." They nodded and turned back towards the exit as they approached it.

* * *

Chuck started climbing first. As he opened up the latch, he looked around and saw no-one. "Alright, all clear. Pass me the cube." Stephen then passed him it up the ladders as Chuck used his free hand to finish opening the hatch. He quickly scrambled out, put the cube down and helped Sarah up, who was the second to climb up. Once Sarah was up he also helped his dad.

"Okay, let's head back to the hotel…" Chuck started before Sarah interrupted him.

"No, we can't go back Chuck, the Fulcrum agent will probably still be watching it like a hawk. We will need to find a new car and start driving east and we can find a hotel at Baker. We can spend the night there and we can wake up early and cross the state line by 8am. Let's go." She started before Chuck stopped her.

"Sarah, come over here behind this bush and change into one of these." He threw her a fulcrum uniform.

"Where did you get these?" She asked.

"While you and my dad were having a heart-to-heart, I found these in the laundry bin." He smirked as he watched her cheeks turn rose red.

"Charles, why are you changing? And why are crossing the border?" Stephen asks.

"Dad, we are rogue, the CIA have ordered Sarah and Casey to put me in a bunker. Sarah took me and we ran. The only way we can lose the CIA, at least for a while, is to fake our deaths." Chuck explained while getting changed behind the bush.

"Okay, how are you going to fake your deaths? What is the cover story?" Stephen asked, almost afraid of what the answer will be.

"We need you to order a drone strike on the bunker and we will have our clothes and phones there when the drone strikes. Then it will look like we tried to destroy the fulcrum base but didn't anticipate the size of the blast, and we got caught in the explosion." Sarah explained as she let Chuck help her get dressed, while also trying not peek at her underwear. _"Chuck, you can look you know."_ She whispered to him.

" _Are you sure?"_ He whispered back. She simply nodded. He opened his eyes and just barely caught himself from staring at her breasts while helping her zip up the jacket as she held her hair up.

"Okay, all done, let's go." Chuck exclaims. They headed towards a parking lot and stole a normal looking car.

* * *

20 minutes later they arrived at a small motel in the Baker. Chuck and Sarah ordered a room with two beds, as they would share a bed and Chuck's dad would take the other.

When they walked into the room, Chuck let Sarah take the first shower while he talked with his dad. "Dad, I know that the last time we saw each other, I wanted the Intersect out of my head but now? I don't think that is a good idea with us being on the run and all." Chuck explains.

"I understand Chuck but where are you going with this?" Stephen asks

"What is different about the 2.0?" Chuck asks.

"Well, obviously the Intel is newer, the cipher is no longer needed, and the host will become a human weapon." Stephen explains.

"How so dad?" Chuck asks.

"It will give the host abilities in skill sets. Say someone tries to punch you, you would instantly know how to perform every single move and combo in boxing. The possibilities are endless." Stephen rambles on, indulged into the topic, clearly enthusiastic about it.

"I want to download it." Chuck says abruptly.

"What? Charles… Are you sure? It is still extremely dangerous, if your retention rate isn't 98 or above it will instantly kill you… Are you sure you want to risk it son?" Stephen already knew the answer but he wanted to be sure.

"Yes dad, I appreciate your concern really but… this is the only way that I can keep Sarah and you safe. I need to do this dad." He says, determined to do the right thing.

"Okay Charles, let me order the drone strike and then we can set it up." Stephen then began to scramble about the room, setting up wires everywhere.

"Chuck? What is your dad doing?" Sarah asks, now only in a t-shirt and panties, as she emerges from the bathroom.

"He is setting up the drone strike and then the 2.0 for upload." Chuck replied, smiling at Sarah.

"Why is he setting it up? Is he planning on uploading it? Is it safe?" Sarah questioned him.

"No… I am. And yeah, it should be safe." Chuck says, looking away from Sarah's eyes.

"What Chuck, why? After all this time of wanting to get it out of your head and starting to live a normal life?" Sarah asks. "What happened to that Chuck?" She quietly adds on.

"Sarah, we are on the run from the CIA and the NSA, I don't think we will ever have a normal life at least not for a long time, and I guess I realised that maybe the life I envisioned for myself was missing something." He tells her.

"What Chuck, what could possibly be missing that would change your mind?" Sarah asks confused.

"You. I realised that when I got the Intersect was out of my head, I would be losing you." He says with his head down.

"Oh. I don't know what to say Chuck." Sarah says surprised.

""Don't say anything, just promise to help me stay me, help me still be the guy that you fell for. Help make sure that I don't turn into someone like Bryce or Casey but instead, help me be like you, able to be an amazing spy, deadly assassin, sexy seductress and still be able to have feelings and care for people. Help me become… The Ultimate Spy." He says, and after he finishes, he kisses her lightly on the lips, to which she aggressively responded by sliding her tongue into his mouth.

* * *

After a long time, they finally ended the battle between their tongues, panting for breath.

" _I love you Sarah Walker, always have."_ He whispers to her.

" _Chuck… I… I…"_ She struggles. He kisses her to stop her. _"Ssshhhh… I know, you can tell me when you're ready."_ He whispers, before letting go of her face and turning to his dad, who had just fired the predator drones missiles.

"Yes, Charles. Fulcrum is now eliminated and Intersect 2.0 is ready for upload. Last chance to back out of this Charles." Stephen warned.

"No, I'm ready for this, I need to do this." Chuck said, obviously not bowing out of this.

"Okay Charles, sit here and begin when you are ready." He then passes Sarah a pair of black glasses. She nods, and puts them on. Stephen does the same and watches as Chuck finger hovers over the enter key.

"Okay, this is it. Goodbye Nerd Herder, hello Super Spy." He then pressed the enter key and watched the flashing images for the fifth time in his life.

He remembers lost memories of a prototype Intersect upload when he was nine, in his father's office.

He remembers solving the riddle in Bryce's email and uploading the 1.0 version of the Intersect.

He remembers putting on a pair of sun glasses and imitating Sean Connery's Bond catch phrase and accidentally uploading an update for the Intersect.

He remembers getting locked to a bed, escaping and accidentally uploading the test version of Fulcrums Intersect.

He remembers being strapped to a chair and being forced to upload the full Fulcrum Intersect.

He remembers sitting on a couch and uploading the Intersect 2.0 as Sarah and his father watched him.

* * *

He wakes to see Sarah looking down at him in the back seat of a car, stroking his head and playing with the curls in his hair. He then notices his head is lying in her lap.

"Good morning Chuck, how did you sleep?"

"What happened?" He asked, sitting up.

"You uploaded the 2.0 then passed out, your dad managed to get a few hours' sleep but I wanted to keep watch, in case we were tailed." She explained.

"I know I shouldn't be but I am extremely tired. Have we crossed the border yet?" He asked.

"Yeah, your dad is driving, we still have another 5-6 hours until we reach his safe house." She says.

"Okay, how about we get some sleep?" Chuck asks.

"No Chuck, I'm fine, plus I don't want to keep you awake." She protested.

"Sarah, I said how about WE get some sleep. I will lie across the seat and you can lie on top of me." He offered.

"Are you sure? I don't want to crush you." She questioned him.

"Na you won't crush me. I'm sure that I will be nice and cosy." He says.

"Okay…" She agrees reluctantly. They then shuffled until she was lying on his back and she was on top of him. The looked at each other and kissed lightly before closing their eyes and falling asleep.

* * *

When they woke up, Stephen was just parking the car beside a cabin in the woods.

"Rise and shine kids, welcome to my humble abode, or rather, our humble abode." He chuckled at that.

They all got out of the car and made their way into the cabin and could see that although it was full of tech, it looked nice and cosy. Chuck walked to the bedroom and fell onto the bed, quickly shedding all of his clothing, except from his boxers.

"Don't stop there Chuck, I told you, when we made it out of there alive, we were going to be a whole lot more than kissing." She said seductively as she stripped naked and stood before Chuck.

"Oh boy." Chuck gulped. Sarah then leaped at him and kissed him passionately as they scrambled under the covers while keeping their lips attached.

* * *

In the other room, Stephen was looking at a computer which numerous files on a organisation called "The Ring" where scattered on it.

"Thank god you found her Charles, because we are going to need all of the help we can get."

"You haven't seen nothing yet."

* * *

 **A/N And there you have it! The beginning of my fourth story. I am NOT quitting any of my other stories I just had this idea in my head and wanted to post this, so here it is. I will probably only update this every now and then as I do want to focus on my other stories but this will definitely be a huge story as we shall see Season's 3 through 5 from Chuck's perspective as he is supposed to be dead.**

 **As always, review please, and without further ado, ADIOS!**


	2. Chapter 2: Pink Slip

_**Disclaimer**_ _ **: I don't own "Chuck"**_

 **Chapter 2: "Versus the Pink Slip"**

* * *

 _Previously on 'Chuck Bartowski: Rogue Spy'_

 _In the other room, Stephen was looking at a computer which numerous files on a organisation called "The Ring" where scattered on it._

 _"Thank god you found her Charles, because we are going to need all of the help we can get."_

 _"You haven't seen nothing yet."_

* * *

 **6 Months Later. Prague.**

A hood is pulled off of a man's head, revealing the man to be Chuck.

"Agent Carmichael." The leader says.

"Call me Charles." Chuck replies. The leader laughs at this.

"You have something that belongs to my boss Yuri. The case, I would like for you to give it to me. Please." Yuri, the leader, laughs mockingly.

"You show up with no gun, and please? I quiver in fear?" He mocks.

"We've got a lock on the case, it's in the room with you." A female voice tells Chuck through an earpiece. Chuck looks around and spots one of the men, holding the case.

He leans forward. "Give me the case… Or else." He threatens with a darker voice.

"Or else what?" All of the men laugh at Chuck's threat. "Or else I do this?" Yuri pulls out his pistol and aims it at Chucks face. Chuck flashes.

"No, I was thinking something more like this." With that, Chuck stands up, grabs Yuri's hand, slams it on the table and pulls the gun out of his grasp. He takes a step back as everyone in the room reaches for their weapons.

"Aaahhh! Cool, cool, cool, everybody be cool, everybody just chill out." He rambles while aiming the gun at Yuri. He looks around the room and says "Very, very good, on the ground now. Nice and easy." He nods towards one of Yuri's henchmen. The henchman slowly puts the gun on the ground.

"Now, Yuri, hand me that case and after that it's Pirogi time." Chuck orders with a humorous voice.

"No…" Yuri replies. _"Shoot him Chuck."_ The feminine voice in his ear tells him.

"Do it, shoot me." Yuri continues, walking around the table towards Chuck.

"Don't mess with me Yuri." Chuck says with a shaky voice, nervous about killing Yuri.

" _Shoot him now."_ The voice in his ear orders.

"Get him." Yuri orders his henchmen.

One man charges at Chuck. Chuck flips the gun in his hand, blocks the man's coming kick and punches him in the face. He then ducks under another of the goons' kick and kicks a chair into another goon, stands up blocking a punch from his attacker and delivering a punch of his own to the goons' face, he then follows that up by jabbing him in the throat with the butt of his gun, knocking the attacker out. He then turns and kicks a gun out of another goons hand, continues spinning and receiving a punch to the face.

Chuck backs up, dazed from the punch. A different goon then kicks him in the stomach, knocking the wind out of Chuck and sending him into the wall. Yuri and the kicker approach Chuck, Chuck swiftly kicks the goon in the stomach, knocking him slightly back into Yuri. Chuck then jumps up and grabs a pipe, swinging from it and kicking both the goon and Yuri in the face, knocking them both out instantly.

" _Chuck what is happening? Your' heart rate just spiked, are you okay?"_ The voice in his ear asks, concerned.

"I'm okay. I got punched in the face. It's throbbing a little bit." Chuck replies, dazed from the hits.

" _Get out of there now!"_ The voice orders. Chuck begins running towards the door, grabbing the case on his way out.

* * *

Chuck runs out into the streets of Prague. "Where's my exit?" He speaks into his watch.

" _They're closing in on you. Get to a roof, a chopper's inbound."_ The voice orders him. Chuck begins running up the street.

As Chuck is running up some stairs, he speaks into his watch. "Listen, Mom, I don't want to souns demanding here… but I could really use that chopper right about now!" He finishes with his voice raised.

" _The chopper is too far out. Satellites say there is a power line on the roof that runs to the next building. Zip line across, we'll find you a new exit…"_ She nearly finishes, but Chuck cuts her off.

"What do you mean zip line?" Chuck asks, voice elevated.

" _It's in the Intersect."_ Chuck's mother informs him.

"Okay, I got this." He says, mainly to himself for reassurance. He proceeds to climb up the roof, nearly falling off.

"Mom, I don't think this is a good idea. I'm not flashing." He rambles, staring at the floor beneath him.

" _Do it Chuck, flash!"_ She encourages him.

"Look if you stress me out, it's never gonna work!" Chuck shouts, terrified.

" _Chuck, flash!"_ His mother shouts again.

"I can't." Chuck squeaks, breathing quickening.

" _Move over, Chuck? Baby it's me."_ A younger, calmer female voice interrupts.

"Sarah?" Chuck pants out, feeling slightly calmer after hearing his girlfriends voice.

" _Yeah, Chuck, it's me. Remember when I was being held hostage outside of the Buy More? And you saved me by jumping off of the roof and swinging down the building using that banner?"_ She asks, using a soothing voice.

"Yeah, what about it?" Chuck asks, his breathing now returning to normal.

" _I need you to flash on that cable and come back to me okay? I need you to come save me again. Chuck, I love you, please come home."_ She sobs, begging him. Her pleading voice brings him to flash. He zip lines across the buildings, landing in the outside area of a café.

"I can't believe that worked." He tells himself.

" _I'm not so sure it did."_ Sarah tells him through his earpiece. Curious, Chuck turns around to see a thug approaching him with a shotgun. He turns back to see another man with a pistol aimed at him. Looking forward he sees Yuri walking towards him, a pistol in his hand. Chuck stands up, with his hand in the air.

"Sarah, there's something I need to tell you." Chuck says, hands still in the air, staring straight at the barrel of Yuri's gun.

" _Not now Chuck."_ Sarah interrupts him.

"Actually, I think this may be my last chance." Chuck says before he hears the sound of a chopper. He looks up to see a stealth chopper flying straight towards him.

"Thank god, Sarah is that ours?" Chuck questions into his watch.

" _No Chuck, run! Casey is on that!"_ Sarah yells at him. Chuck promptly breaks into a sprint, luckily finding an alley to slip into and disappearing into the night. He could still here the faint sounds of Casey's laughter as he fired his minigun at Yuri and his men as he walked towards his own chopper.

* * *

 **12 Hours later.**

 **Undisclosed Location, California**

"Chuck!" Sarah screams and sprints towards him, jumping on him and attacking his lips with a fury that Chuck is slightly scared of.

"Hi… Sarah." Chuck greets her, minutes later, still reeling from the kiss.

"I hate solo missions, they are the worst." Sarah complains. Chuck couldn't agree more.

"Well, now that we have the case, we should be able to move onto more missions that require both of us." Chuck says with a hopeful smile.

"Yeah, hopefully." Sarah returns his smile in full.

"Chuck! What were you thinking out there?! You should of just shot him! It would have been a whole lot easier." Mary complained.

"Don't you dare insult him! If I have anything to say about it he will never has to kill anyone ever!" Sarah growled.

"He needs to learn that being a spy is dangerous and sometimes you need to kill someone, I thought you would know that Agent Walker." Mary sneered.

"Fuck you." Chuck insulted his mother.

"Chuck!" Mary shouted, shocked.

"No, you don't get to insult the woman I love, the bitter-sweet truth is that you don't know me or her. So you don't get to presume jack shit. You left me when I was 9! I haven't seen you in 19 years! You don't know who I am and she knows me better than you ever will." Chuck said.

"You are my son, Charles. Of course I know who you are, you are Charles Irving Bartowski, 28-year-old, born in Encino, raised in LA. You went to Harvard University. You stayed with Ellie and her boyfriend Morgan after Agent Larkin got you kicked out of University." Mary informed her son.

"Sarah can you please correct her?" Chuck asks smugly.

"You are my loving boyfriend, Charles Irving Bartowski, but you prefer to be called Chuck. You recently turned 29, when you told me it was the best birthday ever. You were born in Encino but you moved around as a kid, especially after your dad left you at age 13. The main locations that you stayed where San Diego, Miami, Las Vegas, San Francisco, San Jose and Burbank. You also lived in Palo Alto during your Stanford years. After you were wrongfully removed from Stanford, you stayed with Ellie and her boyfriend Devon "Captain Awesome" Woodcomb. " Sarah informed, growling at Mary for not even knowing her own son's birthday.

"They're all lies. Chuck is 28, I know my son's birthday." Mary says accusingly, looking at Chuck, as if to ask for back-up.

"Actually, mom, I turned 29 four months ago, and Sarah was right, it was definitely the BEST birthday ever." He finished that last sentence with a sly grin, remembering the present he received when we went to bed that night.

"Mary? I need your help down at the lab, I have something to run by you." Stephen said through the intercom.

"On my way Stephen. Goodnight Chuck. I'll debrief you tomorrow properly." With that Chuck and Sarah made their way into their quarters and quickly changed into pajamas.

"Chuck, I just want you to know that you were great today. I think you are ready to become the perfect spy but I will make sure that Mary knows you won't be needing a red test. I like you just the way you are, I don't need some cold heartless killer, what I need is the man I love.

A cute, nerdy, handsome, charming, kind, gentleman-like hero who always does the right thing, whether it's protocol or not, it's what originally intrigued me about you, you were different. You didn't demand sex for cooperation or get all possessive over me whenever someone looked at me the wrong way, you just laid back and accepted that I could take care of myself. So thank you, for being you." She sealed her rant with a sweet, gentle kiss.

"Sarah, I love you too. But I have something I want to read over tonight with you." Chuck patted the spot beside him on the bed, to which Sarah promptly sat down at the spot before laying her head on his chest and snuggling into him.

"Go ahead Chuck." She says.

"I read some files on who the new members or Team Intersect are." He declares.

"Wow Chuck, who is in it? I'm definitely surprised they named their team after you in a way." Sarah says

"Yeah, well, here we go:

Colonel John Casey is the leader of the team.

Agent Carina Miller is the seductress.

Special Agent Daniel Shaw is the Ring expert.

Agent Bryce Larkin is their undercover specialist.

Agent Cole Barker is their international relations expert.

Damn, it seems Beckman has put together a team that consists of everyone who has come into contact with Team Bartowski. Do you think their building an Intersect?" Chuck asks, afraid of the possibility of no longer being the only person who can handle the Intersect.

"Yes and I think they plan on having Bryce upload it." Sarah states.

"It makes sense, Bryce was the second highest score on the retention rate test. I think he got 86%. It's not quite 98% but it would work fairly well for a limited time." Chuck informs her.

"Well, can we please not talk about Bryce in bed?" Sarah pleads, climbing up to straddle Chuck. "In fact, I don't think we should be talking at all." She hints seductively while pulling her camisole over her head, revealing a red lacy bra.

"Nope, no more talking." Chuck says before wrapping his arms around her back and pulling her down to him, and smashing his lips into hers.

* * *

 **6 Months Ago. Barstow.**

As John Casey stared at the item in his hand, he knew this was it. He had failed, not only his job, but to protect the only man that Casey ever thought of as a friend. The friend that never ceased to impress Casey, the man may have been a moron… but he was Casey's moron. And what Casey is looking at right now just isn't right. It shouldn't have come to this.

Casey was staring at Chuck Bartowski's tie, the Nerds tie, _Damn lady feelings, I'll kill the moron next time I see him._ But that wouldn't happen, ever. Because the moron had to go and get himself and the skirt killed, trying to be the hero. _He could never stay in the damn car. Idiot had to go and save his dad instead of just doing as he was told._ This was the first time John Casey has cried in over a decade, and it's all because the skirt and her boy toy couldn't keep it in their pants. _It just wasn't right._ The only way they could have been together was for her to grab the kid and run… now even that has been taken away from them.

"Colonel Casey?" The voice of Casey's superior shook him out of his dazed stupor.

"Yes, ma'am?" He asked after gaining his composure.

"Is it true? Are they gone?" There was a tinge of sadness in her voice.

"Yes ma'am… they're dead ma'am." He replied, barely stifling a sob.

"At least they went out a hero's death. At least we won." Beckman claimed, trying to think of something, anything to change the subject.

"But at what cost?" Casey asked.

"I know John. They didn't deserve to go out like that… but what could we have done?" She asked.

"We could have let them be! We could have let them choose their own choices! We could have let them have what they had been fighting for…" He sighed.

"And what was that John?" Beckman asked him, she knew the answer.

But she needed to here someone who was there to say it.

"All they wanted was to be together. For real, no covers. They were always looking for opportunities to express how they felt for each other. All they needed was for you to let them be together without the risk of being separated. Bartowski was too scared of you to speak up and Walker was far too stubborn to admit she was compromised… but it was so damn obvious." He looked down to hide the small smile on his face, remembering all of the digs he gave them about their lady feelings.

"I was going to let them be together John." She told him, sighing.

"What!?" He asked, shocked at the words that came out of her mouth.

"In the bunker, Chuck would still need a bodyguard, to protect him from any moles that could manage their way to him. If Sarah truly wanted to be with him I would have given them a shared room and everything." She finished her speech with a hint of a smile, imagining their faces when finding out they were sharing a room… and a bed. "He would have needed 24-hour protection… and who better to protect him than the woman who loves him?" She continued.

"Then why not let them have a real relationship outside of the bunker?" Casey asks, confused at his bosses thinking.

"No-one asked me to allow them a real relationship, I was ready to give them a big speech and everything. But they never had the courage to ask me." She looked down.

"What about the 49-B?" Casey questioned.

"It was a test to see if she truly loved him. If she would give up everything she knew to be with him, to protect him. And the sad part is that she passed." Beckman had been berating herself for a while about not just telling them outright to begin a real relationship.

"What now ma'am?" Casey asked.

"Now, we continue fighting. We keep protecting the world in honour of their deaths. We will rebuild Team Intersect with new members to honour Chuck and Sarah. I want you to lead them John. I need you to watch over Bartowski's sister as well. It's what he would have wanted." With that she walked back towards her chopper, got in, and closed the door.

As Casey watches the chopper fly away he feels his phone vibrate, when he pulls his phone out, only two words come to mind.

"Holy shit."

* * *

 **Casey's Apartment. Burbank.**

Casey was sitting down on his chair in his office staring at a video, waiting to be played.

"Well, what do you have for me Bartowski?" He pressed play.

" _My name is Chuck Bartowski and if you're watching this, it means I'm already dead. This is one of the many e-mails that I have recorded tonight and I guess, well, I don't know what to say really, but I'll give it a shot._

 _Casey, buddy, I know that I was a moron and an idiot. But I hope that somewhere deep down you cared for me because I need you to do something for me, I need you to watch over and protect Ellie, Devon and the children I'm sure will be on the way after they eventually marry._

 _I know that I'm asking a lot buddy, but I know you will be able to do it. Think of this as a new mission and remember, Semper Fidelis._

 _I alsoo want to tell you something, you have a daughter Casey. Or rather, Alex Coburn does. When you 'died' your fiancé Kathleen McHugh, was pregnant with a little girl. Her name is Alex McHugh, named after her dad._

 _She is currently in college, she is acing her self-defence class, and is working towards a degree in criminal psychology. She also works down at the pie shack in Burbank._

 _Go to them John, tell them you're alive. Your daughter needs her father. I know you will think that you don't belong there but you need to try. And although Kathleen may hit you a couple times, or if she is anything like you, a lot, you still need to try._

 _I know what it's like growing up without my dad. It is hard, especially the college years, when she is failing her exams and everything seems to be crumbling down around her, she needs her father to swoop in and pick her up, talk to her, give her an inspirational speech, and get her back in there._

 _Goodbye John Casey, I could always count on you catching me when I fell."_

 _(P.S. It's Nerd.)_

* * *

The video end and to say Casey was shocked would be an under-statement.

Bartowski never seemed to amaze him. But one thing Casey was certain.

He was going to tell Kathleen and his daughter he is alive, even if it's the last thing he does. If not for his sake, then for Chuck's.

* * *

 **A/N And there it is! It seems that ALOT of people like this and I had only published one chapter. Definitely loving writing this one, hope you liked the Casey segment. I will be doing more of these flashbacks, they will basically be scenes showing us everyone's reaction to Chuck's 'death'. I can give you a list of all the people who will receive one, but no details.**

 **We have: Beckman, Ellie & Awesome, Bryce & Morgan. Maybe more but can't think of any characters from before the s2 finale that Chuck would have a way to contact, or who is important, but feel free to suggest some. I will be going through this story in episodes. I'm probably going to put Octagon on the back burner just for a couple days as alot of people have been telling me that it isn't as good as my other stories, but if you want me to do anything then be sure to PM me and tell me which stories I should be focusing on.**

 **As always... ADIOS!**


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